Check results for 'ampir'

using R Under development (unstable) (2026-02-12 r89409)
using platform: aarch64-apple-darwin23
R was compiled by Apple clang version 17.0.0 (clang-1700.3.19.1) GNU Fortran (GCC) 14.2.0
running under: macOS Sequoia 15.7.1
using session charset: UTF-8 * current time: 2026-02-13 02:28:26 UTC
checking for file ‘ampir/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘ampir’ version ‘1.1.0’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘ampir’ can be installed ... [7s/7s] OK See the install log for details.
used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
used SDK: ‘MacOSX14.5.sdk’
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [1s/1s] OK
checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
checking whether the package can be unloaded cleanly ... [1s/1s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
checking loading without being on the library search path ... [1s/1s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [3s/3s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking R/sysdata.rda ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking compiled code ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [1s/1s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [2s/2s] ERROR Running ‘testthat.R’ [2s/2s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ampir) > > test_check("ampir") Could not run prediction for 1 proteins because they were either too short or contained invalid amino acids Could not run prediction for 2 proteins because they were either too short or contained invalid amino acids Could not run prediction for 1 proteins because they were either too short or contained invalid amino acids *** caught segfault *** address 0x110, cause 'invalid permissions' *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) 2: kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) 3: as.vector(kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) - b(object)[p]) 4: .SigmoidPredict(as.vector(kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) - b(object)[p]), prob.model(object)[[p]]$A, prob.model(object)[[p]]$B) 5: .local(object, ...) 6: kernlab::predict(modelFit, newdata, type = "probabilities") 7: kernlab::predict(modelFit, newdata, type = "probabilities") 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 12: try(kernlab::predict(modelFit, newdata, type = "probabilities"), silent = TRUE) 13: method$prob(modelFit = modelFit, newdata = newdata, submodels = param) 14: probFunction(method = object$modelInfo, modelFit = object$finalModel, newdata = newdata, preProc = object$preProcess) 15: predict.train(model, df_features[, predictors], type = "prob") 16: FUN(X[[i]], ...) 17: lapply(X = S, FUN = FUN, ...) 18: doTryCatch(return(expr), name, parentenv, handler) 19: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 20: tryCatchList(expr, classes, parentenv, handlers) 21: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 22: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 23: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 24: FUN(X[[i]], ...) 25: lapply(seq_len(cores), inner.do) 26: mclapply(chunks, predict_amps_core, df, model, min_len, mc.cores = n_cores) 27: predict_amps(test_df, n_cores = 2) 28: eval(code, test_env) 29: eval(code, test_env) 30: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) 31: doTryCatch(return(expr), name, parentenv, handler) 32: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 33: tryCatchList(expr, classes, parentenv, handlers) 34: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 35: doWithOneRestart(return(expr), restart) 36: withOneRestart(expr, restarts[[1L]]) 37: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }) 38: test_code(code, parent.frame()) 39: test_that("predict_amps works with multiple cores", { skip_on_os("windows") test_df <- readRDS("../testdata/xbench.rds") result_1core <- predict_amps(test_df, n_cores = 1) expect_equal(dim(result_1core), c(16, 3)) result_2core <- predict_amps(test_df, n_cores = 2) expect_equal(result_1core, result_2core)}) 40: eval(code, test_env) 41: eval(code, test_env) 42: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) 43: doTryCatch(return(expr), name, parentenv, handler) 44: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 45: tryCatchList(expr, classes, parentenv, handlers) 46: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 47: doWithOneRestart(return(expr), restart) 48: withOneRestart(expr, restarts[[1L]]) 49: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }) 50: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) 51: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) 52: FUN(X[[i]], ...) 53: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 58: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) 59: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) 60: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle) 61: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 62: test_check("ampir") An irrecoverable exception occurred. R is aborting now ... Traceback: 1: kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) 2: kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) 3: as.vector(kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) - b(object)[p]) 4: .SigmoidPredict(as.vector(kernelMult(kernelf(object), newdata, xmatrix(object)[[p]], coef(object)[[p]]) - b(object)[p]), prob.model(object)[[p]]$A, prob.model(object)[[p]]$B) 5: .local(object, ...) 6: kernlab::predict(modelFit, newdata, type = "probabilities") 7: kernlab::predict(modelFit, newdata, type = "probabilities") 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 12: try(kernlab::predict(modelFit, newdata, type = "probabilities"), silent = TRUE) 13: method$prob(modelFit = modelFit, newdata = newdata, submodels = param) 14: probFunction(method = object$modelInfo, modelFit = object$finalModel, newdata = newdata, preProc = object$preProcess) 15: predict.train(model, df_features[, predictors], type = "prob") 16: FUN(X[[i]], ...) 17: lapply(X = S, FUN = FUN, ...) 18: doTryCatch(return(expr), name, parentenv, handler) 19: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 20: tryCatchList(expr, classes, parentenv, handlers) 21: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 22: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 23: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 24: FUN(X[[i]], ...) 25: lapply(seq_len(cores), inner.do) 26: mclapply(chunks, predict_amps_core, df, model, min_len, mc.cores = n_cores) 27: predict_amps(test_df, n_cores = 2) 28: eval(code, test_env) 29: eval(code, test_env) 30: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) 31: doTryCatch(return(expr), name, parentenv, handler) 32: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 33: tryCatchList(expr, classes, parentenv, handlers) 34: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 35: doWithOneRestart(return(expr), restart) 36: withOneRestart(expr, restarts[[1L]]) 37: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }) 38: test_code(code, parent.frame()) 39: test_that("predict_amps works with multiple cores", { skip_on_os("windows") test_df <- readRDS("../testdata/xbench.rds") result_1core <- predict_amps(test_df, n_cores = 1) expect_equal(dim(result_1core), c(16, 3)) result_2core <- predict_amps(test_df, n_cores = 2) expect_equal(result_1core, result_2core)}) 40: eval(code, test_env) 41: eval(code, test_env) 42: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) 43: doTryCatch(return(expr), name, parentenv, handler) 44: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 45: tryCatchList(expr, classes, parentenv, handlers) 46: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 47: doWithOneRestart(return(expr), restart) 48: withOneRestart(expr, restarts[[1L]]) 49: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }) 50: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) 51: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) 52: FUN(X[[i]], ...) 53: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 58: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) 59: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) 60: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle) 61: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 62: test_check("ampir") An irrecoverable exception occurred. R is aborting now ... Saving _problems/test-predict-amps-199.R [ FAIL 1 | WARN 1 | SKIP 0 | PASS 82 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-predict-amps.R:197:3'): predict_amps works with multiple cores ── Expected `result_1core` to equal `result_2core`. Differences: `actual` is length 3 `expected` is length 2 `names(actual)`: "seq_name" "seq_aa" "prob_AMP" `names(expected)`: "seq_name" "seq_aa" `actual$prob_AMP` is a double vector (0.0237263013580434, 0.0302258304066241, 0.0433991662785352, 0.0393783553576832, 0.618460240944596, ...) `expected$prob_AMP` is absent [ FAIL 1 | WARN 1 | SKIP 0 | PASS 82 ] Error: ! Test failures. Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [9s/9s] OK
checking PDF version of manual ... [2s/2s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '